SMTL ID : 6kf1.1

Microbial Hormone-sensitive lipase- E53 mutant S162A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-1-mer

Ligands

11 x NPO: P-NITROPHENOL(Non-covalent)

NPO.1: 8 residues within 4Å: Chain A: G.88, A.159, L.190, I.214, F.217, D.218, I.253 Ligands: NPO.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.190, A:F.217 Water bridges: A:D.218, A:R.225 NPO.2: 12 residues within 4Å: Chain A: G.88, F.89, A.160, N.163, L.190, D.218, Y.221, A.223, R.225, G.230, F.231 Ligands: NPO.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.89, A:L.190, A:F.231 Hydrogen bonds: A:G.88, A:A.223, A:R.225 pi-Stacking: A:Y.221 NPO.3: 9 residues within 4Å: Chain A: L.23, Y.35, L.38, V.208, L.209, S.213, F.217, H.281, S.282 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.23, A:Y.35, A:L.38, A:V.208 Water bridges: A:S.213 NPO.6: 12 residues within 4Å: Chain B: G.88, F.89, A.160, N.163, L.190, D.218, Y.221, A.223, R.225, G.230, F.231 Ligands: NPO.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.231 Hydrogen bonds: B:D.218, B:R.225 Water bridges: B:A.223 pi-Stacking: B:Y.221 NPO.7: 10 residues within 4Å: Chain B: G.88, A.159, L.190, L.209, I.214, F.217, D.218, I.253, H.281 Ligands: NPO.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.190, B:F.217, B:F.217, B:I.253 Water bridges: B:R.225 NPO.8: 7 residues within 4Å: Chain B: Y.35, L.38, V.208, L.209, F.217, H.281, S.282 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.35, B:L.38, B:V.208 NPO.11: 12 residues within 4Å: Chain C: G.88, F.89, A.160, N.163, L.190, D.218, Y.221, A.223, R.225, G.230, F.231 Ligands: NPO.12 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.89, C:L.190, C:F.231 Hydrogen bonds: C:G.88, C:D.218, C:A.223 pi-Stacking: C:Y.221 NPO.12: 10 residues within 4Å: Chain C: G.88, A.159, L.190, L.209, I.214, F.217, D.218, I.253, H.281 Ligands: NPO.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.190, C:F.217, C:I.253 NPO.13: 7 residues within 4Å: Chain C: Y.35, L.38, V.208, L.209, F.217, H.281, S.282 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.38, C:V.208 Hydrogen bonds: C:S.282 Water bridges: C:S.213, C:S.213, C:S.213 NPO.16: 10 residues within 4Å: Chain D: G.89, A.160, L.191, L.210, I.215, F.218, D.219, I.254, H.282 Ligands: NPO.17 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.191, D:F.218, D:F.218, D:I.254 Water bridges: D:R.226 NPO.17: 11 residues within 4Å: Chain D: G.89, F.90, A.161, N.164, L.191, D.219, Y.222, A.224, G.231, F.232 Ligands: NPO.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.90, D:F.232 Hydrogen bonds: D:D.219, D:D.219 Water bridges: D:A.224 pi-Stacking: D:Y.222

5 x 6NA: HEXANOIC ACID(Non-covalent)

6NA.4: 4 residues within 4Å: Chain A: A.202, F.203, R.254, R.258 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.202, A:F.203 Water bridges: A:R.258, A:R.258 Salt bridges: A:R.254, A:R.258 6NA.10: 3 residues within 4Å: Chain B: A.198, R.254, R.258 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.198 Water bridges: B:R.254, B:R.258 Salt bridges: B:R.254, B:R.258 6NA.15: 3 residues within 4Å: Chain C: F.203, R.254, R.258 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.203 Water bridges: C:R.254, C:R.254, C:R.258 Salt bridges: C:R.254, C:R.258 6NA.20: 3 residues within 4Å: Chain D: T.28, L.29, E.30 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.29, D:E.30 Hydrogen bonds: D:L.29 6NA.21: 5 residues within 4Å: Chain D: A.199, A.203, F.204, R.255, R.259 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.199, D:A.203, D:F.204 Water bridges: D:R.255, D:R.259 Salt bridges: D:R.255, D:R.259

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 6 residues within 4Å: Chain A: K.262, A.263, E.266 Chain B: K.262, A.263, E.266 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.262, B:K.262, A:K.262, A:K.262 Water bridges: A:A.263

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: M.306, M.307 Chain B: R.299 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.309 Hydrogen bonds: B:R.299

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 2 residues within 4Å: Chain C: R.269 Chain D: E.278 6 PLIP interactions: 6 interactions with chain C Water bridges: C:A.240, C:R.269, C:R.269, C:R.269, C:R.269 Salt bridges: C:R.269 SO4.19: 1 residues within 4Å: Chain D: R.73 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.73

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.18: 6 residues within 4Å: Chain D: S.143, P.144, S.145, G.148, R.149, T.150 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.148 Water bridges: D:T.150, D:T.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiaochen, Y. et al., Functional and Structural Insights into Environmental Adaptation of a Novel Hormone-sensitive Lipase, E53, Obtained from Erythrobacter longus. To Be Published

Release Date

2020-07-08

Peptides

Lipase: ABC
Lipase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Lipase

Lipase